Mercurial > repos > xuebing > sharplabtool
diff tools/fastq/fastq_trimmer.xml @ 0:9071e359b9a3
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| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:37:19 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/fastq/fastq_trimmer.xml Fri Mar 09 19:37:19 2012 -0500 @@ -0,0 +1,120 @@ +<tool id="fastq_trimmer" name="FASTQ Trimmer" version="1.0.0"> + <description>by column</description> + <command interpreter="python">fastq_trimmer.py '$input_file' '$output_file' '${offset_type['left_column_offset']}' '${offset_type['right_column_offset']}' '${offset_type['base_offset_type']}' '${input_file.extension[len( 'fastq' ):]}' '$keep_zero_length'</command> + <inputs> + <param name="input_file" type="data" format="fastqsanger,fastqcssanger" label="FASTQ File"/> + <conditional name="offset_type"> + <param name="base_offset_type" type="select" label="Define Base Offsets as" help="Use Absolute for fixed length reads (Illumina, SOLiD)<br>Use Percentage for variable length reads (Roche/454)"> + <option value="offsets_absolute" selected="true">Absolute Values</option> + <option value="offsets_percent">Percentage of Read Length</option> + </param> + <when value="offsets_absolute"> + <param name="left_column_offset" label="Offset from 5' end" value="0" type="integer" help="Values start at 0, increasing from the left"> + <validator type="in_range" message="Base Offsets must be positive" min="0" max="inf"/> + <validator type="expression" message="An integer is required.">int( float( value ) ) == float( value )</validator> + </param> + <param name="right_column_offset" label="Offset from 3' end" value="0" type="integer" help="Values start at 0, increasing from the right"> + <validator type="in_range" message="Base Offsets must be positive" min="0" max="inf"/> + <validator type="expression" message="An integer is required.">int( float( value ) ) == float( value )</validator> + </param> + </when> + <when value="offsets_percent"> + <param name="left_column_offset" label="Offset from 5' end" value="0" type="float"> + <validator type="in_range" message="Base Offsets must be between 0 and 100" min="0" max="100"/> + </param> + <param name="right_column_offset" label="Offset from 3' end" value="0" type="float"> + <validator type="in_range" message="Base Offsets must be between 0 and 100" min="0" max="100"/> + </param> + </when> + </conditional> + <param name="keep_zero_length" label="Keep reads with zero length" type="boolean" truevalue="keep_zero_length" falsevalue="exclude_zero_length" selected="False"/> + </inputs> + <outputs> + <data name="output_file" format="input" /> + </outputs> + <tests> + <test> + <!-- Do nothing trim --> + <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> + <param name="base_offset_type" value="offsets_absolute"/> + <param name="left_column_offset" value="0"/> + <param name="right_column_offset" value="0"/> + <param name="keep_zero_length" value="keep_zero_length" /> + <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" /> + </test> + <!-- Trim to empty File --> + <test> + <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> + <param name="base_offset_type" value="offsets_absolute"/> + <param name="left_column_offset" value="30"/> + <param name="right_column_offset" value="64"/> + <param name="keep_zero_length" value="exclude_zero_length" /> + <output name="output_file" file="empty_file.dat" /> + </test> + <test> + <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> + <param name="base_offset_type" value="offsets_percent"/> + <param name="left_column_offset" value="50"/> + <param name="right_column_offset" value="50"/> + <param name="keep_zero_length" value="exclude_zero_length" /> + <output name="output_file" file="empty_file.dat" /> + </test> + <!-- Trim to 4 inner-most bases --> + <test> + <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> + <param name="base_offset_type" value="offsets_absolute"/> + <param name="left_column_offset" value="45"/> + <param name="right_column_offset" value="45"/> + <param name="keep_zero_length" value="exclude_zero_length" /> + <output name="output_file" file="fastq_trimmer_out1.fastqsanger" /> + </test> + <test> + <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> + <param name="base_offset_type" value="offsets_percent"/> + <param name="left_column_offset" value="47.87"/> + <param name="right_column_offset" value="47.87"/> + <param name="keep_zero_length" value="exclude_zero_length" /> + <output name="output_file" file="fastq_trimmer_out1.fastqsanger" /> + </test> + </tests> + <help> +This tool allows you to trim the ends of reads. + +You can specify either absolute or percent-based offsets. Offsets are calculated, starting at 0, from the respective end to be trimmed. When using the percent-based method, offsets are rounded to the nearest integer. + +For example, if you have a read of length 36:: + + @Some FASTQ Sanger Read + CAATATGTNCTCACTGATAAGTGGATATNAGCNCCA + + + =@@.@;B-%?8>CBA@>7@7BBCA4-48%<;;%<B@ + +And you set absolute offsets of 2 and 9:: + + @Some FASTQ Sanger Read + ATATGTNCTCACTGATAAGTGGATA + + + @.@;B-%?8>CBA@>7@7BBCA4-4 + +Or you set percent offsets of 6% and 20% (corresponds to absolute offsets of 2,7 for a read length of 36):: + + @Some FASTQ Sanger Read + ATATGTNCTCACTGATAAGTGGATATN + + + @.@;B-%?8>CBA@>7@7BBCA4-48% + +----- + +.. class:: warningmark + +Trimming a color space read will cause any adapter base to be lost. + +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ + + + </help> +</tool>